Because the below floor ballast system is so unique (for the time) and works so well (except for fill/drain times) I would jump through a lot of hoops to fix a leak in mine. That would include all of the above, cutting holes in the floor, cutting the liner in the trunk, whatever. It's just fiberglass, it can be fixed so you can't see it, even if you went in from the outside (I'm not recommending that!)
I have heard of leaks caused by freezing water when the ballast would not empty, i.e. bad solenoid valve. That should be a Toyota warrantee issue, since the tanks are part of the hull/stringer, they should be covered under the lifetime hull warrantee IMHO. You can always pull a line off the tank and drain it. I don't think this procedure is covered in the official winterization procedure in the Toyota owners manual.....